PLOTt: PLOTt, plot RNA-seq and ribo-seq separately.
In hsinyenwu/RiboPlotR: Plot Periodicity of Ribosome Profiling Data

PLOTt

R Documentation

PLOTt, plot RNA-seq and ribo-seq separately.

Description

Plot both RNA-seq and ribo-seq in two plots with a gene model.

Usage

PLOTt(
  YFG,
  RNAbam1 = RNAseqBam1,
  ribo1 = Ribo1,
  ylab1 = Ribolab1,
  SAMPLE1 = S_NAME1,
  CDSonly = FALSE,
  Extend = 50,
  isoform,
  uORF = NULL,
  NAME = "",
  uORFisoform
)

Arguments

`YFG`	Gene ID
`RNAbam1`	Dataset 1 to plot. Default is RNAseqBam1 that was loaded by rna_bam.ribo.
`ribo1`	riboseq dataset
`ylab1`	name of Y-axis
`SAMPLE1`	name of sample 1
`CDSonly`	TRUE or FALSE. Only plot CDS region or all riboseq reads in defined area. Default plot all riboseq reads in the defined area.
`Extend`	Integer. The number of extra nt ploted at the ends of the plots.
`isoform`	Integer. Which isoform to plot periodicity.
`uORF`	Gene ID for uORF
`NAME`	Name of the gene
`uORFisoform`	Isoform number of the uORF